Hi,
Are there any tools that can output the per-base base composition in a non-binary format? I'm looking for something like this:
or alternatively, the total coverage (50 for all POSitions in the above example) with % of each of ACGTNID.
This data can be found/displayed in IGV (coverage track) as in the screenshot here, and probably exported from IGV, but I want to get at this data with a command line tool, without the gui IGV.
Other comments:
- igv count almost does what I want, but I can only seem to load and view its output in IGV.
- coverageBed also almost does what I want, but I don't think it will report the base composition at each position.
- I could parse the samtools mpileup output for the particular POSitions I'm interested in, but I was wondering if this has been implemented already somewhere.
- I also found the thread below, but is quite old
Thanks for your help.
PS I'm new to bioinformatics and apologies if this is trivial.
Are there any tools that can output the per-base base composition in a non-binary format? I'm looking for something like this:
Code:
POS A C G T N I D 1 50 0 0 0 0 0 0 2 0 50 0 0 0 0 0 3 0 25 25 0 0 0 0 4 50 0 0 0 0 0 0 5 0 50 0 0 0 0 0
This data can be found/displayed in IGV (coverage track) as in the screenshot here, and probably exported from IGV, but I want to get at this data with a command line tool, without the gui IGV.
Other comments:
- igv count almost does what I want, but I can only seem to load and view its output in IGV.
- coverageBed also almost does what I want, but I don't think it will report the base composition at each position.
- I could parse the samtools mpileup output for the particular POSitions I'm interested in, but I was wondering if this has been implemented already somewhere.
- I also found the thread below, but is quite old
Thanks for your help.
PS I'm new to bioinformatics and apologies if this is trivial.
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